Prediction of miRNA-disease associations based on strengthened hypergraph convolutional autoencoder

Abstract

Most existing graph neural network-based methods for predicting miRNA-disease associations rely on initial association matrices to pass messages, but the sparsity of these matrices greatly limits performance. To address this issue and predict potential associations between miRNAs and diseases, we propose a method called strengthened hypergraph convolutional autoencoder (SHGAE). SHGAE leverages multiple layers of strengthened hypergraph neural networks (SHGNN) to obtain robust node embeddings. Within SHGNN, we design a strengthened hypergraph convolutional network module (SHGCN) that enhances original graph associations and reduces matrix sparsity. Additionally, SHGCN expands node receptive fields by utilizing hyperedge features as intermediaries to obtain high-order neighbor embeddings. To improve performance, we also incorporate attention-based fusion of self-embeddings and SHGCN embeddings. SHGAE predicts potential miRNA-disease associations using a multilayer perceptron as the decoder. Across multiple metrics, SHGAE outperforms other state-of-the-art methods in five-fold cross-validation. Furthermore, we evaluate SHGAE on colon and lung neoplasms cases to demonstrate its ability to predict potential associations. Notably, SHGAE also performs well in the analysis of gastric neoplasms without miRNA associations.

Keywords: Association prediction; Graph neural network; miRNA–disease associations.